[show abstract][hide abstract] ABSTRACT: Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here, we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity and is protected wherever it is considered native. Small populations of this species are located in Iberia, where they are unprotected because they are considered introductions due to their rarity. However, Iberia and neighbouring regions in southwestern France have been shown to support discrete glacial refuge populations of many European trees, and the possibility remains that Iberian white elms are native relicts. We used chloroplast RFLPs and nuclear microsatellites to establish the relationship between populations in Iberia and the Central European core distribution. Bayesian approaches revealed significant spatial structure across populations. Those in Iberia and southwestern France shared alleles absent from Central Europe, and showed spatial population structure within Iberia common in recognized native taxa. Iberian populations show a demographic signature of ancient population bottlenecks, while those in Central European show a signature of recent population bottlenecks. These patterns are not consistent with historical introduction of white elm to Iberia, and instead strongly support native status, arguing for immediate implementation of conservation measures for white elm populations in Spain and contiguous areas of southern France.Heredity advance online publication, 11 September 2013; doi:10.1038/hdy.2013.81.
[show abstract][hide abstract] ABSTRACT: Sub-arctic willow scrub is an endangered habitat in Britain, and typically occurs on steep crags inaccessible to grazing animals.
These willows can reproduce both sexually and asexually, although the relative importance of each is unknown. Knowledge of
reproductive mode is important for the design of grazing management and restoration programmes. Accordingly, clonality was
assessed in the largest stand of sub-arctic willow scrub in the UK, focusing on Salix lanata and S. lapponum. Little evidence of clonal growth was detected; most individuals possessed distinct multi-locus genotypes. Thus despite the
capacity for vegetative reproduction, and seedlings being rarely observed, sexual reproduction is the predominant means of
perpetuation and dispersal at this site. We also examined clonal growth in a common willow species (Salix herbacea) that occupies a different habitat type (exposed mountain tops and ridges). Multiple individuals shared identical genotypes
up to 7 m apart, suggesting an important role for clonal growth in local patch formation in this species.
Plant Systematics and Evolution 04/2012; 269(1):75-88. · 1.31 Impact Factor
[show abstract][hide abstract] ABSTRACT: In Britain the genus Euphrasia comprises ca 20 diploid and tetraploid plant species, including several endemics. However, their conservation is impeded by taxonomic
uncertainty. Analysis of cpDNA and AFLP variation was used to assess their taxonomic status and establish the extent of barriers
to gene exchange among them. Differences in ploidy level constitute a very strong barrier to genetic exchange, although this
is not absolute. The diploid endemics E. vigursii and E. rivularis form morphologically and genetically definable units which show some level of reproductive isolation. Within tetraploid Euphrasia, the species showed varying degrees of distinctness. Analysis of geographically paired samples from two widespread outcrossing
taxa E. arctica and E. nemorosa provides evidence for extensive genetic exchange between them. However AFLP data indicate that this outbreeding species complex
possesses a gene pool distinct from that of the widespread inbreeding tetraploids. The widespread and endemic inbreeding tetraploids
contain examples of morphologically and genetically definable taxa, but also species whose distinctness is more equivocal.
The conservation implications of this study are that species-based action plans are potentially suitable for conservation
of the diploid endemics E. vigursii and E. rivularis. In contrast we contend that a species-based conservation framework, developed with reproductively isolated and genetically
distinct groups in mind, requires modification for conservation of the complex and dynamic diversity found within the tetraploids.
The adoption of ‘taxonomic’ action plans, designed to protect the evolutionary processes generating Euphrasia diversity, may provide a supplementary solution for conserving this type of variation.
[show abstract][hide abstract] ABSTRACT: Although often considered as evolutionary dead ends, selfing taxa may make an important contribution to plant evolution through hybridization with related outcrossing lineages. However, there is a shortage of studies examining the evolutionary dynamics of hybridization between outcrossing and selfing taxa. On the basis of differential pollinator attractiveness, production and competitive ability of pollen, as well as levels of inbreeding depression, we predict that the early products of hybridization between outcrossing and selfing lineages will be F1s and first-generation backcrosses sired mainly by the outcrossing lineage, together with selfed F2s containing a limited genetic contribution from the outcrosser. These predictions were tested using amplified fragment length polymorphism and chloroplast markers to analyze the composition of a recent hybrid swarm between predominantly outcrossing Geum rivale and predominantly selfing Geum urbanum. In line with predictions, the hybrid swarm comprised both parental species together with F1s and first-generation backcrosses to G. rivale alone. Chloroplast data suggested that G. rivale was the pollen parent for both observed hybrid classes. However, there was no evidence for F2 individuals, despite the fact that the F1 was fully self-compatible and able to auto-pollinate. The pollen fertility of F1s was only 30% lower than that of the parental taxa, and was fully restored in backcross hybrids. Predicting future evolution in the hybrid swarm will require an understanding of the mating patterns within and among the mix of parental, F1 and backcross genotypes that are currently present. However, these results support the hypothesis that introgression is likely to be asymmetrical from selfing to outcrossing lineages.
[show abstract][hide abstract] ABSTRACT: Genetic variation in Epipactis helleborine in the British Isles was assessed using starch gel electrophoresis of isozymes; 273 individuals were sampled from 13 populations and examined for genetic variation using eight enzyme systems encoded for by 13 loci. Overall, 46% of the loci examined were polymorphic, with an average of 1.69 alleles per locus. Within populations, a mean of 33% of the loci were polymorphic, with a mean number of 1.46 alleles per locus. Levels of genetic variation were compared between urban and well established rural populations to assess the genetic consequences of colonization of the urban sites. The average levels of genetic variation detected in urban populations were lower than that found in rural populations, although there was a much greater range of variation among the urban populations. Large urban populations actually have patterns of variation similar to rural populations and show evidence of multiple founders. This indicates that the high dispersibility of Epipactis seeds can in some cases overcome the predicted loss of genetic variation associated with founder effects during colonization. Small urban populations, however, show significantly lower levels of genetic variation compared with these large urban populations and the rural populations, and it seems likely that this is attributable to single founding events and/or genetic drift.
Botanical Journal of the Linnean Society 05/2008; 123(4):321 - 331. · 2.59 Impact Factor
[show abstract][hide abstract] ABSTRACT: The early genetic effects of habitat degradation were investigated in the critically endangered conifer Araucaria nemorosa. This species occurs in New Caledonia, a global biodiversity hotspot where the world's greatest concentration of endemic conifer species coincides with an extremely high level of habitat destruction due to fire and mining. Using seven microsatellite loci, estimates were made of genetic marker variation, inbreeding coefficients and population differentiation of adult and seedling cohorts of A. nemorosa. These were contrasted with equivalent estimates, made over similar spatial scales and with the same marker loci, in the locally common and more widespread sister species Araucaria columnaris. There were no significant differences in population genetic parameters between adult populations of the two species, despite their different abundances. However, in A. nemorosa, the juvenile cohort showed a loss of rare alleles and elevated levels of inbreeding when compared to the adult cohort. These genetic differences between the cohorts were not observed in the locally common A. columnaris. This suggests that recent environmental degradation is influencing the genetic structure of A. nemorosa populations. Although this is not detectable among predisturbance adult populations, an early warning of these impacts is evident in more recently established seedling cohorts. The conservation implications of these results are discussed.
[show abstract][hide abstract] ABSTRACT: A set of expressed sequence tag–simple sequence repeat (EST-SSR) loci has been developed for Arabidopsis lyrata ssp. petraea. From 768 root cDNA clones, 126 microsatellites, including di-, tri-, tetra- and pentanucleotide repeat motifs were identified and primers were designed to 24 EST-SSRs. Eleven loci were subsequently screened on 150 individuals sampled from five natural populations, which revealed three to nine alleles per locus (mean 5.36) and expected heterozygosity (HE) estimates ranging from 0.046 to 0.698. Significant deviations from random mating were observed at 10 EST-SSR loci, likely due to inbreeding (global FIS = 0.151) and population structure (global FST = 0.246). Scottish Executive Environmental and Rural Affairs Department
[show abstract][hide abstract] ABSTRACT: The liverwort Anastrophyllum joergensenii Schiffn., reported from Norway, Scotland, Alaska and the Sino-Himalaya is shown to consist of two distinct species, A. alpinum Steph. (treated before as a synonym of A. joergensenii) in the Himalaya, western China, Alaska and Scotland, and A. joergensenii Schiffn. s. str. in Norway, Scotland and western China. The two species are distinguished on genetic characters, size, leaf and perianth characters, and appear to have different ecological preferences. Anastrophyllum alpinum, although the more widespread of the two in Scotland, is there known only as non-fertile plants, whereas in the Sino-Himalaya fertile populations and sporophytes are not infrequent; in contrast, the rarer A. joergensenii can produce perianths in Scotland, Norway and Yunnan but androecia and sporophytes are unknown. The differences between the two are detailed and the ecology and distribution outlined.
Journal of Bryology 05/2006; 28(2):108-117. · 1.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: The genetic structure of populations of an arctic-montane herb, Saxifraga hirculus (Saxifragaceae), was analysed by means of chloroplast restriction fragment-length polymorphism. Sampled populations were distributed across Europe and North America (Alaska and Colorado). There was no evidence for geographically structured genetically divergent lineages, and although no haplotypes were shared between North America and Europe, the haplotypes from different continents were intermixed on a minimum spanning tree. European populations were much more highly differentiated and had much lower levels of haplotype diversity than their Alaskan counterparts. Centres of haplotype diversity were concentrated in those Alaskan populations located outside the limits of the last (Wisconsin) glaciation, suggesting that they may have acted as refugia during the Pleistocene. It was not possible to identify putative migration routes or corresponding refugia in the European genepool. One British population, from the Pentland Hills, was genetically very distant from all the others, for reasons that are as yet unknown.
[show abstract][hide abstract] ABSTRACT: Restoration of scrub and woodland in deforested upland sites is an important conservation activity. However, little is known about the mycorrhizal colonisation potential of upland soils or the factors that influence the distribution of mycorrhizal inoculum. We investigated the effect of existing vegetation on mycorrhizal colonisation potential for a sub-arctic willow (Salix lapponum) by planting uninoculated cuttings into plotsrepresenting two upland habitats with either grassand herbs (‘grass’) or Vaccinium myrtillus (‘vaccinium’) and assessing mycorrhizal colonisation after 14 months using morphological and molecular techniques. From 40 willow cuttings (20 in each habitat), DNA sequences of rive ectomycorrhizal (EcM) fungal taxa were recovered: Laccaria proxima, Thelephora terrestris, Hebeloma sp., ‘Thelephoraceae sp.’ and ‘Pezizales sp.’. Cuttings in the ‘grass’ habitat were dominated by Laccaria proxima and ‘Pezizales sp.’ and in the ‘vaccinium’ habitat by Thelephora terrestris which was absent from the ‘grass’ habitat. There were no significant differences between habitats in frequency of EcM inoculum (overall percentage of cuttings colonised = 70%) or colonisation potential (overall mean percentage of root tips colonised per cutting = 20 %). These data suggest that the mycorrhizal colonisation potential and diversity of fungi available to willow in these upland soils are low and planted willow may benefit from inoculum enhancement.
Botanical Journal of Scotland 01/2006; 58(1):19-34.
[show abstract][hide abstract] ABSTRACT: To examine the performance and information content of different marker systems, comparative assessment of population genetic diversity was undertaken in nine populations of Athyrium distentifolium using nine genomic and 10 expressed sequence tag (EST) microsatellite (SSR) loci, and 265 amplified fragment length polymorphism (AFLP) loci from two primer combinations. In range-wide comparisons (European vs. North American populations), the EST-SSR loci showed more reliable amplification and produced more easily scorable bands than genomic simple sequence repeats (SSRs). Genomic SSRs showed significantly higher levels of allelic diversity than EST-SSRs, but there was a significant correlation in the rank order of population diversities revealed by both marker types. When AFLPs, genomic SSRs, and EST-SSRs are considered, comparisons of different population diversity metrics/markers revealed a mixture of significant and nonsignificant rank-order correlations. However, no hard incongruence was detected (in no pairwise comparison of populations did different marker systems or metrics detect opposingly significant different amounts of variation). Comparable population pairwise estimates of F(ST) were obtained for all marker types, but whilst absolute values for genomic and EST-SSRs were very similar (F(ST) = 0.355 and 0.342, respectively), differentiation was consistently higher for AFLPs in pairwise and global comparisons (global AFLP F(ST) = 0.496). The two AFLP primer combinations outperformed 18 SSR loci in assignment tests and discriminatory power in phenetic cluster analyses. The results from marker comparisons on A. distentifolium are discussed in the context of the few other studies on natural plant populations comparing microsatellite and AFLP variability.
[show abstract][hide abstract] ABSTRACT: The genus Euphrasia in Britain comprises a taxonomically complex group of self-compatible, morphologically similar, hemi-parasitic, annual plant species of high conservation importance. The 19 diploid and tetraploid taxa currently recognised show striking variation in flower size. The objective of this paper is to determine whether a relationship exists between flower size and breeding system within Euphrasia. Following a survey of flower size variation among the 19 taxa, seven diploid populations, encompassing a broad range of flower sizes, were selected for detailed study. Four nuclear microsatellite loci were used to estimate the inbreeding coefficient Fis within each population. Fis values varied from to 0.17-0.77 and showed a significant, negative correlation with flower size. These results are best explained as the consequence of variation in selfing rate among the Euphrasia populations, with selfing rate increasing as flower size decreases. The potential factors influencing breeding system evolution in Euphrasia are discussed, together with the role of autogamy in generating taxonomic complexity and facilitating lineage differentiation within the genus.
[show abstract][hide abstract] ABSTRACT: Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high.
[show abstract][hide abstract] ABSTRACT: The enormous losses suffered by the European elms during recent Dutch elm disease outbreaks led to concern over the conservation of elm genetic resources, and the subsequent establishment of a series of ex situ collections. However, as ex situ collections are inevitably finite in size, some consideration needs to be given to selecting which samples to include in them. To contribute towards this process for European ex situ elm collections we have undertaken genetic studies on a Europe-wide sample of 535 individuals. A major aim has been to use genetic markers to clarify the identification of samples to ensure that the ex situ collections contain a representative spread of taxonomic diversity. This is important given the paucity of mature elms in the landscape due to Dutch elm disease. The lack of mature material (critical for identification) compounds identification problems in what was already a taxonomically difficult group. Our data (derived from random amplified polymorphic DNA and inter-simple sequence repeats) have provided a useful supplement to morphology in undertaking such sample identifications. The molecular data served to highlight mis-identified samples and led to extensive revisions of sample identities within individual countries. Our results were less useful in detecting regional intra-specific genetic structure, and do not provide sufficient information for prioritising within-species sample selections.
[show abstract][hide abstract] ABSTRACT: Population genetic theory for 'traditional' codominant loci showing low levels of allelic diversity (eg allozymes) has been well characterised and evaluated. In contrast, appropriate methods for the analysis of data from more recently developed marker systems are still being refined. For multilocus dominant markers such as amplified fragment length polymorphisms (AFLPs) and randomly amplified polymorphic DNA (RAPDs), the methods of data analysis can be split into two main categories. In population-based approaches, population allele frequencies are compared to obtain some measure of the partitioning of genetic diversity into within- and between-population components. In contrast, individual-based approaches use individual multilocus genotypes as the unit of analysis. Inferences on population processes such as gene flow are based on inter-relationships among individual samples as visualised on phenetic diagrams such as neighbour joining trees. Using a simulation approach coupled with neighbour joining analyses, we show that while the underlying population genetic structure is an important determinant of tree shape in the analysis of dominant data, the number of loci examined also affects the topology. At low levels of population differentiation (eg FST=0.07), mutually exclusive clustering of individuals into their respective populations can occur when sufficiently large numbers of loci are scored (eg 250 loci, typical of many AFLP studies). In contrast, unresolved star-shaped topologies can be recovered at higher levels of population differentiation (FST= >0.15) when lower numbers of loci are employed (eg 50 loci, typical of many RAPD studies). Thus, the relationship between tree topology and the extent of genetic structuring of populations is contingent upon the number of dominant loci scored. The consequences of these findings for the biological interpretation of individual-based analysis of dominant data sets are discussed.
[show abstract][hide abstract] ABSTRACT: Spiranthes romanzoffiana Cham. is restricted in Europe to the British Isles, where it is recognised as a conservation priority species due to frequent extirpation of populations along with no evidence of seed set; vegetative reproduction has been invoked as the sole means of perpetuation and dispersal. To investigate the reproductive ecology of this species, 17 populations have been sampled for chloroplast microsatellites and amplified fragment length polymorphisms (AFLPs). These markers revealed a previously unsuspected genetic-geographic split in the species, which correlates with differences in patterns of within-population variation. Northern populations were fixed for one chloroplast haplotype but showed high levels of AFLP genotypic diversity consistent with sexual reproduction (proportion of genotypes distinguishable, PD = 0.98). More southerly populations showed fixed differences from the northern populations in their chloroplast haplotype and for 10 AFLP markers. They harboured only 12 unique multilocus genotypes among 113 individuals from six populations (PD = 0.11). These genotypes differed mostly by single bands, and none by more than 4/138 loci, with identical multilocus genotypes occurring in widely separated populations. This uniformity in southern populations is consistent with agamospermous or autogamous reproduction, and/or an extreme population bottleneck. Finally, the observed patterns of population differentiation in S. romanzoffiana are compared with other studies of orchids, revealing a wide range of values that belie recent contrasting published generalisations that claim that orchids show either higher, or lower, levels of population differentiation than other plant families.
[show abstract][hide abstract] ABSTRACT: Euphrasia species in Britain attract a large amount of conservation attention due to the recognition of numerous endemic taxa in what is essentially a species-poor flora. To develop a set of research tools to investigate the evolutionary processes underlying this diversification, a membrane enrichment procedure has been used to isolate five polymorphic microsatellite loci from Euphrasia nemorosa (Pers.) Wallr. These loci amplify polymorphic products in several other British Euphrasia species.
[show abstract][hide abstract] ABSTRACT: The attributes of codominance, reproducibility and high resolution have all contributed towards the current popularity of nuclear microsatellites as genetic markers in molecular ecological studies. One of their major drawbacks, however, is the development phase required to obtain working primers for a given study species. To facilitate project planning, we have reviewed the literature to quantify the workload involved in isolating nuclear microsatellites from plants. We highlight the attrition of loci at each stage in the process, and the average effort required to obtain 10 working microsatellite primer pairs.
[show abstract][hide abstract] ABSTRACT: The utility of EST-simple sequence repeats (EST-SSRs) was evaluated in the fern Athyrium distentifolium. From 1152 frond cDNA clones, 165 microsatellites, including di-, tri-, tetra and penta-nucleotide repeat motifs, were identified. Primer design was possible for 74 of the SSRs; subsequent screening of 10 loci on 186 individuals from six natural populations revealed between two and seven alleles per locus and expected heterozygosity (HE) estimates ranging from 0.027 to 0.809. Eight of these loci were further examined for cross-species and cross-generic amplification in other Woodsiaceae species, and polymorphic products were detected. EST-derived SSRs provide robust, informative and potentially transferable polymorphic markers suitable for biodiversity research.